Docking studies of Tau Protein by pengxiuhui


									            IAENG International Journal of Computer Science, 33:1, IJCS_33_1_7

                                    Docking studies of Tau Protein
          Harkewal Singh, Dr. Soma S. Marla, Manas Agarwal, Jaypee University of Information Technology,
                                      Waknaghat, Solan (H.P.) India 173215

       Abstract-Alzheimer’s disease (AD)[1] is a fatal          (medial temporal lobe) that causes the first
       brain disorder and alone in United States                symptoms.
       approximately 4.5 millions Americans are suffering       The neurons are involved in the travel of electric
       from this disease which is expected by 2050 to           charges, resulting in the release of messages. AD
       range between 11.3 million to 16 million[2]
       Alzheimer’s disease is a form of dementia, in which
                                                                disrupts this intimate signaling system, resulting
       nerve cells in memory areas of brain and                 into formation of abnormal Senile Plaque (made
       eventually other areas begin to die at accelerated       of β-amyloid. [6]
       rate resulting in serious deterioration in several       Neurofibrillary Tangles are abnormal collections
       mental functions, such as loss in memory,                of twisted threads found inside nerve cells. The
       language, orientation and judgment [3]                   main component of the tangles is one form of the
       AD is characterized by the formation of senile           protein tau. Tau protein has the ability to bind
       plaques (made of β amyloid, a toxic protein that         and stabilize the cells’ internal skeleton called
       comes from normal protein) and neurofibrillary           microtubule. In neuron, cells that are healthy
       tangles (followed by changes in tau protein)
                                                                microtubules form structures like train tracks,
       resulting in neuronal destructions. Currently
       available drugs against AD target the acetylcholine      which guide nutrients and molecules from the
       cycle thus stopping the abnormal breakdown of            centre bodies of the cells down to the end of the
       acetylcholine.        The       modern        docking    axons. Tau normally forms the connector pieces
       programs/software packages e.g. MOE, AcSite,             of the microtubule tracks. In the cells which are
       Spdbv, and Rastop etc can be used to find the            affected by AD, the train track structures
       active site of the tau protein [4]. The ligand against   collapses, tau is changed chemically and can no
       this active binding site can be found by MOE. The        longer hold the pieces together [7]. A changed
       exact confirmation and configuration of the ligand       form of a protein kinase hyper phosphorylates
       can be calculated to find the best molecule with
                                                                tau and causes cytoskeleton to collapse. This
       minimum binding energy [5] and it can be used to
       develop potential drug molecules against the             collapse of the transport system first may result
       disease. This work is an attempt to find out the         in malfunctions in communication between nerve
       amino acid sequences responsible for biologically        cells and later lead to neuron death. Tau is also
       active structure which should enable us to design a      known as Beta 2 transferrin, desialated
       lead molecule against the disease.                       transferrin. Tau is a Cerebro-Spinal Fluid[8],[9].
       In this work we have carried out the docking
       analysis of Tau protein responsible for AD. 50           Drugs like tacrine (Cognex®), donepezil
       structures after the docking were saved in the form      (Aricept®), rivastigmine (Exelon®), or
       of a database. The best five structures in terms of
                                                                galantamine (Razadyne®, formerly known as
       energy were taken, and the amino acids residues of
       the ligand and receptor molecule which bind to           Reminyl®) memantine (Namenda®) [10]
       give the best biologically active conformation, were     available today target β-amyloid, as the possible
       analyzed.                                                drug receptor protein for Alzheimer’s disease.
       Index Terms—Alzheimer’s disease, Docking, MOE            But reports suggest that tau protein is also
        Tau Protein                                             responsible for the occurrence of Alzheimer’s
                                                                disease by forming the neurofibrillary tangles
                        I. INTRODUCTION                         [11].
       The symptoms of Alzheimer’s disease appear
       due to the loss of nerve cells in certain regions of             II. MATERIALS AND METHODS
       the brain, principally the cerebral cortex, and the      In this work we attempted to carry out the
       part that controls our higher mental functions.          docking of Tau protein with the following
       The degeneration of these nerve cells leads to a         infrastructure.
       loss of millions of the connections (synapses)           A. SYSTEM USED - Intel® Pentium® 4, 1.80
       between nerve cells; it is the loss of connections       GHz, 256 MB RAM
       in the part of the brain dealing with memory

                               (Advance online publication: 13 February 2007)
Windows XP Pro 2002 Service Pack 2, Red Hat
MOE (Molecular Operating Environment)
Rastop, Spdbv (3D molecular viewer), Acsite
D. PROTEIN - (Tau protein)
1J1B.pdb, 2BTP.pdb

The abnormal functioning of tau proteins; and
hence the formation of tangles should be             Fig. 2 – Various parameters employed in Energy
controlled by blocking the active sites of the       Minimization of protein Molecule.
target protein. The active sites were found using
AcSite and MOE tools. The 3D structures of the       The minimized structure was used as the
active site were viewed by using tools like          template for Docking.
Rastop, Spdbv, etc.
The amino acid sequence was retrieved using          B. Docking
MOE software and several ligand molecules            The binding of the ligand molecule with the
were designed against the active site by targeting   protein molecule was analyzed using MOE
these amino acids.                                   docking program to find the correct confirmation
                                                     (with the rotation of bonds, structure of molecule
A. Energy Minimization                               is not rigid) and configuration (with the rotation
The energy of the protein molecule was               of whole molecule, structure of the molecule
minimized using the Energy minimization              remains rigid) of the ligand, so as to obtain
algorithm of MOE tool. The minimized                 minimum energy structure.J1B.pdb, 2BTP.pdb
structures were saved as &              consists of two ligand molecules, so the docking in the working directory.               was performed separately for each of the ligands.
                                                     The parameters used for the Docking are:—
                                                     Total Runs = 50
                                                     Cycle/Runs = 15
                                                     Iteration Limit = 10,000
                                                     Potential Energy Grid: ON
                                                     Annealing Algorithm: Simulated Annealing

1A-         1B- 2btp_min.moE
Fig. 1 - 1A and 1B Showing Minimized
Structures in MOE window

The following parameters were used for energy
Gradient = 0.05
Force Field: MMFF94X + Solvation
                                                     Fig. 3 – MOE window shown Docking
Chiral Constraint: Current Geometry
                                                     Parameters employed

                                                     We saved a total 50 structures in the database.
                                                     The active site of the receptor was found using
                                                     MOE and docking was performed by selecting
                                                     the active site.
C. Calculating the active Site Sequence
The pocket sequence of the active site was
calculated by using active site finder tool of

                                                  Fig. 6 - MOE window showing Flexible
                                                  Alignment Parameters
                                                  Configuration Limit=1000, Alpha=2.5, Gradient
                                                  Test=0.01, RMSD Tolerance=0.5, Maximum
                                                  Steps=500, Iteration Limit=500, Failure Limit =
                                                  30, Energy Cut-Off = 10, Rigid Body

Fig. 4 - MOE window showing parameters used       a)-1J1B
in Alpha Site Finder                              RED CHAIN-Chain A
Probe Radius 1 = 1.4, Probe Radius 2 = 1.8,       Ile28-Gly29-Asn30-Gly31-Ser32-Phe33-Gly34-
Isolated     Donor/Acceptor=3,      Connection    Val36-Ala49-Lys51-Val76-Leu98-Asp99-
Distance = 2.5, Minimum Site Size = 3, Radius =   Tyr100-Val101-Thr104-Arg107-Asp147-
2                                                 Lys149-Gln151-Asn152-Leu154-Asp166-
                                                  GREEN CHAIN- Chain B
                                                  b) - 2BTP
                                                  RED CHAIN -Chain A
                                                  GREEN CHAIN-Chain B
Fig. 5 –Dock box around the active site and the   Leu167-Asn168-Val171-Leu207-Ile208-Leu211-
database generated.                               Asn215-Leu218
D. Flexible Alignment                                           IV. CONCLUSIONS
The best five of the ligand structures from the   Ser32 is the differentiating residue between the
database were imported in MOE to analyze the      two chains of 1JIB whereas in 2BTP both chains
common part of the ligand. This was achieved by   are similar to each other. This has been
the Flexible Alignment tool of MOE. Following     confirmed by Alpha Site finder of MOE as well
parameters were used to calculate the flexible    as Acsite.
alignment (Fig. 6)                                The docking results were confirmed with Patch
Many possible structures for the ligand were      Dock, (clustering RMSD 4.0) Version beta1.2.
generated using MOE, and the best five (having    This works on shape complementarity principles.
minimum energy) were considered as the            The contact analysis of Protein and Ligand has
possible ligand molecules against the target      been performed using Sequence Editor and
proteins (i.e. 1J1B & 2BTP).                      Protein Contact Modules of MOE. The Ligand of
Each pdb has two chains which are shown in the    1J1B has ANP_430 and ANP_930 residues
figure as green and red respectively. Five best   while the ligand of 2BTP has PRO_7, ALA_6,
ligands against the two chains of 1JIB and 2BTP   SEP_5, ARG_4, GLN_3 AND ARG_2 residues.
were generated after the docking. The amino       It suggests that NZ atom of LYS85 of 1J1B and
acid sequence for the pocket site was found as    O1A atom of ANP430 of 1st and 3rd chain of
following –                                       1JIB are interacting with each other by
                                                  hydrogen bonds.
           (a)                                     (b)                                     (c)
Fig. 7 – MOE window showing the flexible alignment of best five ligands (a)-1JIB-green chain, (b)-
1JIB-Red Chain & (c)- 2BTP-Red and green Chain; to find out the common region of ligands

     (a)                                           (b)                                             (c)
  Fig. 8 – MOE Window showing the Ligands of 1JIB (a)-green chain (b)-red chain and 2BTP both

The same kind of bonding is between the                  Ligand for 2BTP has again two types of
following residues of 1st and 3rd chain of 1J1B-         interactions viz. Hydrogen Bonding and Ionic
O atom of ASP133 and N6 of ANP430,                       Interactions. The complete information regarding
O atom of GLN185 and O3 of ANP430,                       the interactions is available in the table 2 of
OD2 of ASP200 and N3B of ANP430                          appendix For ANP we can get top 30 drugs
While there are Ionic Interaction between NZ             information from RCSB. Most of the drugs have
atom of LYS85 and O1A atom of ANP430,                    similarity with the structure of ANP. So it can be
NZ atom of LYS183 and O3G of ANP430.                     very well inferred that an analogous molecule
ANP 930 has again two kinds of Interactions viz.         from the database can be helpful to replace the
Hydrogen Bonding and Ionic.                              existing ligand.
Between following residues there are hydrogen
bonding interactions –                                                V. OBSERVATIONS
NZ atom of LYS585 and O1A atom of ANP930
O atom of ASP633 and N6 atom of ANP930                   The most important interactions which involve
NZ atom of LYS683 and O3G atom of ANP930                 ligand and receptor’s active site are hydrogen
O atom of GLN685 and O3G atom of ANP930                  bonding and ionic. These suggest that new ligand
OD2 atom of ASP700 and N3B atom of ANP930                should be generated keeping in view that it
both of second and third chain of 1J1B                   should be able to have stronger hydrogen and
respectively.                                            ionic interaction with the amino acid moieties of
Ionic Interactions for ANP930 are as following           the binding site. Also there is no disulphide
NZ atom of LYS585 and O1A atom of ANP930,                linkage between the two so the ligand should not
NZ atom of LYS681 and O3G atom of ANP930,                have groups which can avail these interactions
of second and third chain of 1J1B respectively.          easily. The smiles string of the ligands is
Complete Description is shown in the table 1             achieved from MOE which can give the actual
given in appendix.                                       structure of the ligand. The Chemical formula of
                                                         ANP can be found from RCSB which shall help
us to build new ligand(s) to block the abnormal
functionality of the Tau protein imparted due to
the existing ligand.

Table 1 describes about the protein contact
analysis report of 1JIB and Table 2 about 2BTP.

The authors would like to thank Dr. Yaj Medury,
Vice Chancellor (JUIT), and Dr. Naveen
Prakash, Director (JUIT) for their moral and
financial support in carrying out the work. We
would also like appreciate Mr. Deeptak Verma
of JUIT for helping in the formatting of the

[1].Selkoe, D. J. (1997) Science 275, 630-631
[2].Alzheimer’s Disease Fact sheet, NIH
publication no. 03-3431 December 2005
[3].Vani Rao, Constantine G. Lyketsos,
Delusions      in    Alzheimer's    Disease,    J
Neuropsychiatry Clinical Neurosciences 10:373-
382, November 1998
[4].MOE        (The      Molecular      Operating
Environment) Version 2005.06, Chemical
Computing                                  Group
[5].Molecular Modeling - Principles and
Applications, Andrew R. Leach
[6]. Wang, R., Sweeney, D., Gandy, S. E., and
Sisodia, S. S. (1996) J. Biol. Chem. 271, 31894-
[7].Gail V. W. Johnson and William H.
Stoothoff, Tau phosphorylation in neuronal cell
function and dysfunction, Journal of Cell
Science 117, 5721-5729 (2004)
[8].Psychiatric News January 3, 2003
Volume 38 Number 1
[9]. Sussmuth SD, Reiber H, Tumani H, Tau
protein in cerebrospinal fluid (CSF): a blood-
CSF barrier related evaluation in patients with
various neurological diseases, Neuroscience
Letter, 2001 March 9; 300(2):95-8.
[10]Experimental Alzheimer drugs targeting
beta-amyloid and the “amyloid hypothesis, Fact
Sheet: Nov 30, 2005
[11].Adriana Ferreira, Tau protein needed for
Alzheimer’s disease, NUIN news, 2002
                               Table 1 – Protein Contact Report of 1JIB.pdb

Protein Contacts Report
Fri Apr 21 09:34:03 2006
Contact types:
Ionic bonds
Hydrophobic contacts
Hydrogen bonds
Disulfide bonds

Do not report contacts within chains
Report contacts between different chains of like tags
Report inferred contacts of sequence-only data

Conservation          :    1
Sequence separation   :    4
Network separation    :    0
Ionic cutoff          :    4.5
Hydrophobic cutoff    :    4.5
Disulfide cutoff      :    2.5
HIS is Basic          :    TRUE
MET is Hydrophobic    :    TRUE
H bond between main and    sidechain   : TRUE

3     1J1B     TRANSFERASE

     Type   Chain      Pos   Residue        Chain      Pos   Residue      Net
1     HB    1:1J1B.A    32   SER66.OG       2:1J1B.B   242   ASP764.OD2    14
2     HB    1:1J1B.A   181   SER215.OG      2:1J1B.B   266   TYR788.OH     12
3     HB    1:1J1B.A   182   TYR216.OH      2:1J1B.B   268   GLU790.OE1    11
4     HB    1:1J1B.A   230   ASP264.OD2     2:1J1B.B    44   SER566.OG     13
5     HB    1:1J1B.A   254   TYR288.OH      2:1J1B.B   193   SER715.OG     10
6     HB    1:1J1B.A    51   LYS85.NZ       3:1J1B       1   ANP430.O1A     2
7     HB    1:1J1B.A    99   ASP133.O       3:1J1B       1   ANP430.N6      2
8     HB    1:1J1B.A   151   GLN185.O       3:1J1B       1   ANP430.O3*     2
9     HB    1:1J1B.A   166   ASP200.OD2     3:1J1B       1   ANP430.N3B     2
10    HB    2:1J1B.B    63   LYS585.NZ      3:1J1B       2   ANP930.O1A     1
11    HB    2:1J1B.B   111   ASP633.O       3:1J1B       2   ANP930.N6      1
12    HB    2:1J1B.B   161   LYS683.NZ      3:1J1B       2   ANP930.O3G     1
13    HB    2:1J1B.B   163   GLN685.O       3:1J1B       2   ANP930.O3*     1
14    HB    2:1J1B.B   178   ASP700.OD2     3:1J1B       2   ANP930.N3B     1
15    HYD   1:1J1B.A    33   PHE67.CE2      2:1J1B.B   245   VAL767.CG2     8
16    HYD   1:1J1B.A   183   ILE217.CG2     2:1J1B.B   241   VAL763.CG1     9
17    HYD   1:1J1B.A   229   VAL263.CG1     2:1J1B.B    45   PHE567.CZ      3
18    HYD   1:1J1B.A   229   VAL263.CG2     2:1J1B.B   195   ILE717.CG2     3
19    HYD   1:1J1B.A   233   VAL267.CG2     2:1J1B.B    45   PHE567.CE2     3
20    ION   1:1J1B.A   226   ASP260.OD1     2:1J1B.B   198   ARG720.NE      7
21    ION   1:1J1B.A   256   GLU290.OE2     2:1J1B.B    74   ARG596.NH1     6
22    ION   1:1J1B.A   256   GLU290.OE2     2:1J1B.B   158   ARG680.NH2     6
23    ION   1:1J1B.A    51   LYS85.NZ       3:1J1B       1   ANP430.O1A     5
24    ION   1:1J1B.A   149   LYS183.NZ      3:1J1B       1   ANP430.O3G     5
25    ION   2:1J1B.B    63   LYS585.NZ      3:1J1B       2   ANP930.O1A     4
26    ION   2:1J1B.B   161   LYS683.NZ      3:1J1B       2   ANP930.O3G     4
                                 Table 2 – Protein Contact Report of 2BTP.pdb

Protein Contacts Report
Fri Apr 21 09:39:38 2006

Contact types:
Ionic bonds
Hydrophobic contacts
Hydrogen bonds
Disulfide bonds
Do not report contacts within chains
Report contacts between different chains of like tags
Report inferred contacts of sequence-only data

Conservation          :    1
Sequence separation   :    4
Network separation    :    0
Ionic cutoff          :    4.5
Hydrophobic cutoff    :    4.5
Disulfide cutoff      :    2.5
HIS is Basic          :    TRUE
MET is Hydrophobic    :    TRUE
H bond between main and    sidechain    : TRUE


     Type   Chain        Pos   Residue       Chain      Pos   Residue     Net
4     HB    1:2BTP.A     100   TYR82.OH      2:2BTP.B    17   ARG18.NE      3
6     HB    1:2BTP.A     107   GLU89.OE1     2:2BTP.B    17   ARG18.NH1     3
7     HB    1:2BTP.A      71   LYS49.NZ      3:2BTP.P     6   PRO7.O        9
8     HB    1:2BTP.A      78   ARG56.NH1     3:2BTP.P     4   SEP5.O3P      1
9     HB    1:2BTP.A     145   ARG127.NH1    3:2BTP.P     4   SEP5.O1P      1
10    HB    1:2BTP.A     146   TYR128.OH     3:2BTP.P     4   SEP5.O2P      1
11    HB    1:2BTP.A     191   ASN173.OD1    3:2BTP.P     5   ALA6.N        8
12    HB    1:2BTP.A     242   ASN224.ND2    3:2BTP.P     3   ARG4.O       10
13    HB    2:2BTP.B      48   LYS49.NZ      4:2BTP.Q     6   PRO7.O        9
14    HB    2:2BTP.B      55   ARG56.NH1     4:2BTP.Q     4   SEP5.O3P      1
15    HB    2:2BTP.B     122   ARG127.NH1    4:2BTP.Q     4   SEP5.O1P      1
16    HB    2:2BTP.B     123   TYR128.OH     4:2BTP.Q     4   SEP5.O2P      1
17    HB    2:2BTP.B     168   ASN173.OD1    4:2BTP.Q     5   ALA6.N        8
18    HB    2:2BTP.B     215   ASN224.ND2    4:2BTP.Q     3   ARG4.O       10
25    ION   1:2BTP.A     107   GLU89.OE1     2:2BTP.B    17   ARG18.NH1    12
26    ION   1:2BTP.A      71   LYS49.NZ      3:2BTP.P     6   PRO7.O        5
27    ION   1:2BTP.A      78   ARG56.NH1     3:2BTP.P     4   SEP5.O3P      2
28    ION   1:2BTP.A     145   ARG127.NH1    3:2BTP.P     4   SEP5.O1P      2
29    ION   2:2BTP.B      48   LYS49.NZ      4:2BTP.Q     6   PRO7.O        5
30    ION   2:2BTP.B      55   ARG56.NH1     4:2BTP.Q     4   SEP5.O3P      2
31    ION   2:2BTP.B     122   ARG127.NH1    4:2BTP.Q     4   SEP5.O1P      2

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